import jalview.analysis.AlignmentUtils;
import jalview.io.FastaFile;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
-import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
*/
public class Alignment implements AlignmentI
{
- protected Alignment dataset;
+ private Alignment dataset;
protected List<SequenceI> sequences;
- protected List<SequenceGroup> groups = java.util.Collections
- .synchronizedList(new ArrayList<SequenceGroup>());
+ protected List<SequenceGroup> groups;
protected char gapCharacter = '-';
public boolean hasRNAStructure = false;
- /** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
- HiddenSequences hiddenSequences = new HiddenSequences(this);
+ HiddenSequences hiddenSequences;
public Hashtable alignmentProperties;
- private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+ private List<AlignedCodonFrame> codonFrameList;
private void initAlignment(SequenceI[] seqs)
{
- int i = 0;
+ groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
+ hiddenSequences = new HiddenSequences(this);
+ codonFrameList = new ArrayList<AlignedCodonFrame>();
- if (jalview.util.Comparison.isNucleotide(seqs))
+ if (Comparison.isNucleotide(seqs))
{
type = NUCLEOTIDE;
}
type = PROTEIN;
}
- sequences = java.util.Collections
- .synchronizedList(new ArrayList<SequenceI>());
+ sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
- for (i = 0; i < seqs.length; i++)
+ for (int i = 0; i < seqs.length; i++)
{
sequences.add(seqs[i]);
}
seqs[i] = new Sequence(seqs[i]);
}
+ initAlignment(seqs);
+
/*
- * Share the same dataset sequence mappings (if any). TODO: find a better
- * place for these to live (alignment dataset?).
+ * Share the same dataset sequence mappings (if any).
*/
- this.setCodonFrames(al.getCodonFrames());
-
- initAlignment(seqs);
+ if (dataset == null && al.getDataset() == null)
+ {
+ this.setCodonFrames(al.getCodonFrames());
+ }
}
/**
}
@Override
- public void setDataset(Alignment data)
+ public void setDataset(AlignmentI data)
{
if (dataset == null && data == null)
{
}
else if (dataset == null && data != null)
{
- dataset = data;
+ if (!(data instanceof Alignment))
+ {
+ throw new Error(
+ "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+ }
+ dataset = (Alignment) data;
for (int i = 0; i < getHeight(); i++)
{
SequenceI currentSeq = getSequenceAt(i);
@Override
public void addCodonFrame(AlignedCodonFrame codons)
{
- Set<AlignedCodonFrame> acfs = getCodonFrames();
- if (codons != null && acfs != null)
+ List<AlignedCodonFrame> acfs = getCodonFrames();
+ if (codons != null && acfs != null && !acfs.contains(codons))
{
acfs.add(codons);
}
* @see jalview.datamodel.AlignmentI#setCodonFrames()
*/
@Override
- public void setCodonFrames(Set<AlignedCodonFrame> acfs)
+ public void setCodonFrames(List<AlignedCodonFrame> acfs)
{
if (dataset != null)
{
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
@Override
- public Set<AlignedCodonFrame> getCodonFrames()
+ public List<AlignedCodonFrame> getCodonFrames()
{
+ // TODO: Fix this method to fix failing AlignedCodonFrame tests
+ // this behaviour is currently incorrect. method should return codon frames
+ // for just the alignment,
+ // selected from dataset
return dataset != null ? dataset.getCodonFrames() : codonFrameList;
}
@Override
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
- Set<AlignedCodonFrame> acfs = getCodonFrames();
+ List<AlignedCodonFrame> acfs = getCodonFrames();
if (codons == null || acfs == null)
{
return false;
@Override
public void append(AlignmentI toappend)
{
- if (toappend == this)
- {
- System.err.println("Self append may cause a deadlock.");
- }
- // TODO test this method for a future 2.5 release
+ // TODO JAL-1270 needs test coverage
// currently tested for use in jalview.gui.SequenceFetcher
boolean samegap = toappend.getGapCharacter() == getGapCharacter();
char oldc = toappend.getGapCharacter();
.getFullAlignment().getSequences() : toappend.getSequences();
if (sqs != null)
{
+ // avoid self append deadlock by
+ List<SequenceI> toappendsq = new ArrayList<SequenceI>();
synchronized (sqs)
{
for (SequenceI addedsq : sqs)
}
}
}
- addSequence(addedsq);
+ toappendsq.add(addedsq);
}
}
+ for (SequenceI addedsq : toappendsq)
+ {
+ addSequence(addedsq);
+ }
}
AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
for (int a = 0; alan != null && a < alan.length; a++)
addAnnotation(alan[a]);
}
+ // use add method
getCodonFrames().addAll(toappend.getCodonFrames());
List<SequenceGroup> sg = toappend.getGroups();
* Parameters control whether gaps in exon (mapped) and intron (unmapped)
* regions are preserved. Gaps that connect introns to exons are treated
* conservatively, i.e. only preserved if both intron and exon gaps are
- * preserved.
+ * preserved. TODO: check caveats below where the implementation fails
*
* @param al
+ * - must have same dataset, and sequences in al must have equivalent
+ * dataset sequence and start/end bounds under given mapping
* @param preserveMappedGaps
* if true, gaps within and between mapped codons are preserved
* @param preserveUnmappedGaps
boolean preserveUnmappedGaps)
{
// TODO should this method signature be the one in the interface?
- int count = 0;
boolean thisIsNucleotide = this.isNucleotide();
boolean thatIsProtein = !al.isNucleotide();
if (!thatIsProtein && !thisIsNucleotide)
{
return AlignmentUtils.alignProteinAsDna(this, al);
}
-
- char thisGapChar = this.getGapCharacter();
- String gap = thisIsNucleotide && thatIsProtein ? String
- .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
- : String.valueOf(thisGapChar);
-
- // TODO handle intron regions? Needs a 'holistic' alignment of dna,
- // not just sequence by sequence. But how to 'gap' intron regions?
-
- /*
- * Get mappings from 'that' alignment's sequences to this.
- */
- for (SequenceI alignTo : getSequences())
+ else if (thatIsProtein && thisIsNucleotide)
{
- count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
- preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
+ return AlignmentUtils.alignCdsAsProtein(this, al);
}
- return count;
+ return AlignmentUtils.alignAs(this, al);
}
/**
}
return hasValidSeq;
}
+
+ /**
+ * Update any mappings to 'virtual' sequences to compatible real ones, if
+ * present in the added sequences. Returns a count of mappings updated.
+ *
+ * @param seqs
+ * @return
+ */
+ @Override
+ public int realiseMappings(List<SequenceI> seqs)
+ {
+ int count = 0;
+ for (SequenceI seq : seqs)
+ {
+ for (AlignedCodonFrame mapping : getCodonFrames())
+ {
+ count += mapping.realiseWith(seq);
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Returns the first AlignedCodonFrame that has a mapping between the given
+ * dataset sequences
+ *
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ @Override
+ public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo)
+ {
+ for (AlignedCodonFrame acf : getCodonFrames())
+ {
+ if (acf.getAaForDnaSeq(mapFrom) == mapTo)
+ {
+ return acf;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+ {
+ int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
+ int startPos = alignmentStartEnd[0];
+ int endPos = alignmentStartEnd[1];
+
+ int[] lowestRange = new int[] { -1, -1 };
+ int[] higestRange = new int[] { -1, -1 };
+
+ for (int[] hiddenCol : hiddenCols)
+ {
+ lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+ higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ }
+
+ if (lowestRange[0] == -1 && lowestRange[1] == -1)
+ {
+ startPos = alignmentStartEnd[0];
+ }
+ else
+ {
+ startPos = lowestRange[1] + 1;
+ }
+
+ if (higestRange[0] == -1 && higestRange[1] == -1)
+ {
+ endPos = alignmentStartEnd[1];
+ }
+ else
+ {
+ endPos = higestRange[0] - 1;
+ }
+ return new int[] { startPos, endPos };
+ }
}
git://source.jalview.org / jalview.git / blobdiff